The Who, What, When, Where and Why of Chemistry
Chemistry is not a world unto itself. It is woven firmly into the fabric of the rest of the world, and various fields, from literature to archeology, thread their way through the chemist's text.

Learning to tell time when I grew up was a challenge. Clocks were analog - not digital. Everywhere. I can still see the little stiff pink paper clocks we were issued in first grade, with a brass brad fastening the hands to the face. We practiced setting the hands and reading off the time. Thanks to LCDs (liquid crystal displays) my sons had a quantiative sense of time much earlier, digital clocks blinked at them in every corner of their lives.

It took quite a bit to turn the initial discovery into a technology so smoothly integrated into modern life that we rarely notice it's there (how many LCD screens are in the room where you are now? Don't forget the ones in your pockets...). You can read more about the history of the LCD in this blog post by Ben Gross, a fellow at the CHF where I'm currently a short term fellow.

One of the pivotal developments was the leveraging of the twisted nematic effect...which made me wonder what worms (nematodes) and my iPad might have in common. The Greek root of threads....

Chemists are the Zen masters of science. Chemistry is a minimalist art. Its structures and mechanisms resemble the spare ink characters which trickle down scrolls. We seek elegant syntheses in which a few, carefully chosen pieces collapse into a whole. There is particular pleasure chemists take in crafting a molecule that strains the bounds of possibility — such as cubane — which evokes the aesthetic of Noh, where nearly impossible movements are made to look effortless. And despite our abilities to peer into the depths of a molecule with lasers or beams of neutrons, we haven't lost our connection our history. We are still distilling and crucibles are not merely historical artifacts. Zen sees a beauty in the old and well-used, a touch of wabi.

I've a piece in this month's Nature Chemistry on what makes a molecule beautiful (here, $), through the lens of the ten molecules that I consider to be most beautiful. I've already had a couple of emails suggesting gorgeous molecules that didn't make my list. What's on your list of elegant molecules?

Elemental naming was as fraught in the 19th century as it can be today (though now the IUPAC has rules and committees). Alternate names and symbols for elements persisted not merely for decades, but in some cases more than a century.

I've recently skimmed a number of articles about glucinium (Gl). Not familiar? It has 4 protons and these days is known as beryllium for the gemstone beryl, in which it can be found. Beryllium salts can taste sweet, hence glucinium. Beryllium was suggested early on an option, since the sweet taste of its salts was not a unique characteristic. Other metals, including lead and yttrium, form sweet tasting salts. Still, in 1890 many authors were insisting that glucinium was the preferred name, suggesting that the arguments were continuing nearly a century after the initial discovery. It took more than 150 years for the chemistry community to settle on beryllium.

Other elements have endured dueling names, including colombium (now niobium) and the sounds-too-awkward-to-be-real jargonium (hafnium!).

In searching for an appropriate image, Google turns up lots of bathtubs, including this one. Not only does an antiquated elemental name appear in the description of this wild tub, but the term angstrom as well. Translation software, I'm sure, but what is being (mis)translated?

I ran across a reference to aqua fortis in one of the commentaries in Chemical News (1891). The conversation is about a suit in court where a chemist was injured when an inappropriately packaged bottle of aqua fortis spilled. (It had a cork, and according to the rather snarky commentator, the judge — and the chemist in question — should have known that aqua fortis should not be capped with a cork.)

Aqua fortis, literally strong water, was once the common name for nitric acid. Concentrated nitric acid is a strong oxidizing agent (I can still see the small scar on my mother's hand from a spill in her undergraduate days), and I imagine would rather quickly eat away any organic matter, such as a cork. Glass would obviously be the preferred medium for storage. The suit is a frivolous one!

The term aqua fortis has fallen out of fashion, but its companion term has not: aqua regia, the royal water that would dissolve even gold. Aqua regia, as any general chemistry text will tell you, is a mix of concentrated nitric acid and concentrated hydrochloric acid (a 1:3 ratio by volume). Neither acid alone with dissolve gold (or a variety of other hard to oxidize metals), but the trick lies in the shifting equilibria.

Nitric acid is able to oxidize small amounts of gold, turning elemental gold into ions, Au3+. These ions then react with the chloride ions from the hydrochloric acid to form the complex ion AuCl4—. As the gold ions are pulled into the chloroaurate complex, the nitric acid oxidizes a bit more elemental gold. This goes on until all the solid elemental gold has been turned in chloroaurate ions floating around in solution. Imagine putting out a bowl of pretzels, as the pretzels get eaten, you try to keep it full by adding more pretzels. Eventually you run out of pretzels. The trick of using complex ion formation to drive something that isn't very soluble into solution is a common one.

Arguably the most famous example of this happened when the Nazis invaded Copenhagen. Franck and von Laue had given their 23 karat Nobel prize medals to Bohr to prevent the Nazis from confiscating them. Bohr was reluctant to bury them, sure that wherever they were hidden, a search would eventually turn them up. A chemist on staff, de Hevesy, thought to use aqua regia to dissolve the medals. After the war the gold was precipitated out and recast into medals; Franck received his recast medal in the early 1950s. Those were strong waters indeed that Bohr and de Hevesy waded into.

Bruce Gibb mused in a Thesis column in Nature Chemistry a few months back about taking small chunks of time to tune up your research apparatus. I'm on sabbatical leave this semester, and in addition to the research projects I've got going, I'm trying to devote some time on a regular basis to just this. I'm playing with an simple animation app, that would let me quickly put together animations for research talks or classes — and test driving apps for electronic research notebooks.

As a computational chemist, I've been balanced on the knife edge of digital record keeping my whole career. What goes into paper archives (hand kept, or printed), what stays electronic? Who backs stuff up, how often? Long term storage? I've encourage my students to think about how they want to track their data and, at least as importantly, their thinking about their data. Through it all (from punch cards to mag tape to memory sticks) I've always kept at least some of my work on real paper, in a traditional hardbound notebook. In ink. Dated. You know the drill.

I've been reluctant to let go of pen and paper. Just as I still outline just about any piece of writing, including this one, on real paper, I find I think differently off the keyboard. Keyboards tend to enforce a certain linearity of thinking, while a sheet of paper (or several and lots of stickies) lets me move into multiple dimensions, with fewer restrictions on insertions and more flexibility in formatting.

The work I'm doing now in the archives is facilitated by having photos of what I'm reading, many of the bound copies are too fragile to routinely scan or photocopy. Ironically, reading 19th century journals has catapulted me into the 21st century as far as my own record keeping is concerned. I'm using an integrated notebook app on my iPad which allows me to scribble and sketch by hand, take and incorporate photos (and mark them up if I wish), and input text from the keyboard. Finally, I can tag pages, and filter the notebook by tags (more consistent than my own hand written indexing procedures). The only thing I don't care for is that I can't write as small as I wish, making it harder to get an overall view of where I'm going. It's an experiment still,

Today's Nature [Nature481, 410(2012)] has an editorial and an analysis piece on digital record keeping in science. One scientist notes that paper has nothing to offer her - she's gone entirely to her iPad. I may be right behind.

The late 19th and early 20th centuries were hotbeds of elemental discoveries (literally and figuratively). New elements came — and on occasion went. Some were known elements in unknown guises, such as previously unrecognized allomorphs. Others, like didymium, weren't elements at all, but mixtures of as yet to be identified elements (in this case neodymium and praseodymium). Some were more ephermeral than others.

Yesterday I ran across a description of the discovery of a new element in an 1890 issue of Chemical News: damarium, oddly enough reported in the Notes & Queries section and not among the research papers. The report of the gaseous element, collected in Damara Land (present day Namibia) was a bit over the top, even for a time when flowery prose was in style in scientific papers: "One of the party had in his hat a branch of a shrub, which in a very short time lost its green colour and assumed a violet blue..."

One contemporary report assumes it is a hoax, but several sources were not so quick to dismiss the claim, particularly in a period when elemental identity was in flux. At least one commenter wondered if it might be "helium" — an element as yet undiscovered on earth.

I wonder if it's worth tracking down the original cite if I can (the Chemiker Zeitung is available on microfilm at the Othmer). Ah...Google books has it here.

I am currently wending my way through fragile but fascinating volumes of Chemical News - a journal published by Sir William Crookes in the late 19th and early 20th century. It was a major journal at the time, looking rather like the current Nature in it's breadth of coverage. The society journals of the time typically reserved their pages for papers read by members and abstracts of papers thought to be of interest to them, while Chemical News and it's ilk included book reviews, reports of papers from a wide swath of journals in several languages and two robust arenas for conversation between scientists, readers and editors: Correspondence and Notes & Queries. They were a bit more open, too, to offer space to offbeat bits of science.

The volume I just finished (1890) has a rather contentious conversational thread winding through the Correspondence on what it means to be a FCS (Fellow of the Chemical Society) and should membership be more tightly policed vis a vis their chemical credentials. (At one point the secretaries of the Chemical Society accuse a former board member of having used fake letterhead to secure support for his position!) Many participants in the conversation resort to pseudonyms, some of which carry a bit of snark with them, and it's interesting that this controversy is playing out primarily in a commercial journal and not in organs internal to the Society.

My project involves tracking the correspondence around primary reports of research findings, so these raucous conversations, while fun reads, are of peripheral interest. I'll admit to finding other interesting tidbits to tag in my electronic notebook. It doesn't pay to be overly focussed when doing archive work, as long as I can avoid being completely dragged down the rabbit hole.

The Notes & Queries section appears just above the one page of adverts included in each issue, and yesterday this ad caught my eye: "The Benzene Nucleus. — An India-rubber Stamp in nickel-plated locket with ink-pad enclosed" 3s. At the top of the page, the last bit of editorial content appears — a report of a curious invention: a stamp for making benzene rings. The first benzene ring in a journal appeared in Chemical News (in 1879, eight years after the first graphical structure was used), so perhaps it's apt that it report this "little contriviance" in its pages. (And the inventor is a Fellow of the Chemical Society!)

Nowadays chemical structure drawing programs are commonplace, but when I was a graduate student chemical structures had to be hand drawn, using India ink (permanent, not water soluble!) on vellum. The Rapidograph pens used were expensive and notorious for getting clogged (irreversibly so). Rings were made using stencils, text added using mechanical lettering guides. Jiggle your hand and you had trouble that white-out might not be able to rescue you from. Blots? Argh.

I don't miss the days of chancy ink drawings for slide and papers, though I do miss the delight of pulling out pens and ink and paper. I do wonder, though, if note taking organic students would appreciate a little ink stamp of a benzene ring on the end of their pencil or pen?